This paper presents an extension to a heuristic method for phasing and imputation of genotypes of descendants in biparental populations so that it can phase and impute genotypes of parents that are ungenotyped or partially genotyped. The imputed genotypes of the parent are used to impute low-density (Ld) genotyped descendants to high density (Hd). The extension was implemented as part of the AlphaPlantImpute software and works in three steps. First, it identifies whether a parent has no or Ld genotypes and identifies its relatives that have Hd genotypes. Second, using the Hd genotypes of relatives, it determines whether the parent is homozygous or heterozygous for a given locus. Third, it phases heterozygous positions of the parent by matching haplotypes to its relatives. We measured the accuracy (correlation between true and imputed genotypes) of imputing parent genotypes in simulated biparental populations from different scenarios. We tested the imputation accuracy of the missing parent's descendants using the true genotype of the parent and compared this with using the imputed genotypes of the parent. Across all scenarios, the imputation accuracy of a parent was >0.98 and did not drop below ∼0.96. The imputation accuracy of a parent was always higher when it was inbred than outbred. Including ancestors of the parent at Hd, increasing the number of crosses and the number of Hd descendants increased the imputation accuracy. The high imputation accuracy achieved for the parent translated to little or no impact on the imputation accuracy of its descendants.

中文翻译：

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双亲植物群体缺失亲本单核苷酸多态性数据的定相和估算

本文提出了一种启发式方法的扩展，用于对双亲群体中后代的基因型进行定相和估算，以便它可以对未基因型或部分基因型的父母的基因型进行定相和估算。亲本的推算基因型用于将低密度 (Ld) 基因型后代推算为高密度 (Hd)。该扩展作为 AlphaPlantImpute 软件的一部分实施，分三个步骤进行。首先，它确定亲本是否没有或 Ld 基因型，并确定其亲属是否具有 Hd 基因型。其次，使用亲属的 Hd 基因型，确定亲本对于给定基因座是纯合还是杂合。第三，它通过将单倍型与其亲属相匹配来定相亲本的杂合位置。我们测量了不同场景下模拟双亲群体中估算亲本基因型的准确性（真实基因型和估算基因型之间的相关性）。我们使用父母的真实基因型测试了缺失父母后代的估算准确性，并将其与使用父母的估算基因型进行比较。在所有场景中，父母的插补准确度均 >0.98，并且没有低于 ∼0.96。近交亲本的插补准确度总是高于远交亲本。包括 Hd 处亲本的祖先，增加杂交数量和 Hd 后代数量可以提高插补的准确性。父代获得的高插补精度对其后代的插补精度影响很小或没有影响。